RAG2 (recombination activating 2)

Gene

• Entrez ID: 5897
• Gene name: Recombination activating 2
• Gene symbol: RAG2
• Synonyms (NCBI Gene): RAG-2
• Chromosome: 11
• Chromosome location: 11p12
• Summary: This gene encodes a protein that is involved in the initiation of V(D)J recombination during B and T cell development. This protein forms a complex with the product of the adjacent recombination activating gene 1, and this complex can form double-strand b

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1288430	hsa-miR-142-5p	CLIP-seq
MIRT1288431	hsa-miR-154	CLIP-seq
MIRT1288432	hsa-miR-186	CLIP-seq
MIRT1288433	hsa-miR-299-3p	CLIP-seq
MIRT1288434	hsa-miR-3133	CLIP-seq
MIRT1288435	hsa-miR-3185	CLIP-seq
MIRT1288436	hsa-miR-340	CLIP-seq
MIRT1288437	hsa-miR-383	CLIP-seq
MIRT1288438	hsa-miR-410	CLIP-seq
MIRT1288439	hsa-miR-4276	CLIP-seq
MIRT1288440	hsa-miR-4648	CLIP-seq
MIRT1288441	hsa-miR-4654	CLIP-seq
MIRT1288442	hsa-miR-4769-5p	CLIP-seq
MIRT2085492	hsa-miR-1225-5p	CLIP-seq
MIRT2085493	hsa-miR-4314	CLIP-seq
MIRT2085494	hsa-miR-4455	CLIP-seq
MIRT2085495	hsa-miR-4477b	CLIP-seq
MIRT2085496	hsa-miR-496	CLIP-seq
MIRT2085497	hsa-miR-555	CLIP-seq
MIRT2085498	hsa-miR-609	CLIP-seq
MIRT1288436	hsa-miR-340	CLIP-seq
MIRT2607216	hsa-miR-513a-3p	CLIP-seq
MIRT2607216	hsa-miR-513a-3p	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
HMGA1	Unknown	15713121
LEF1	Unknown	12244173
MYB	Unknown	12044781
PAX5	Unknown	11094072;12044781

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002313	Process	Mature B cell differentiation involved in immune response	IEA
GO:0002326	Process	B cell lineage commitment	IEA
GO:0002331	Process	Pre-B cell allelic exclusion	IEA
GO:0002331	Process	Pre-B cell allelic exclusion	ISS
GO:0002358	Process	B cell homeostatic proliferation	IEA
GO:0002360	Process	T cell lineage commitment	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003682	Function	Chromatin binding	IEA
GO:0003682	Function	Chromatin binding	ISS
GO:0005546	Function	Phosphatidylinositol-4,5-bisphosphate binding	IEA
GO:0005546	Function	Phosphatidylinositol-4,5-bisphosphate binding	ISS
GO:0005547	Function	Phosphatidylinositol-3,4,5-trisphosphate binding	IEA
GO:0005547	Function	Phosphatidylinositol-3,4,5-trisphosphate binding	ISS
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IEA
GO:0005654	Component	Nucleoplasm	TAS
GO:0006310	Process	DNA recombination	IEA
GO:0006325	Process	Chromatin organization	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008270	Function	Zinc ion binding	ISS
GO:0030183	Process	B cell differentiation	IEA
GO:0030183	Process	B cell differentiation	ISS
GO:0030217	Process	T cell differentiation	IEA
GO:0033077	Process	T cell differentiation in thymus	IEA
GO:0033077	Process	T cell differentiation in thymus	ISS
GO:0033085	Process	Negative regulation of T cell differentiation in thymus	IEA
GO:0033151	Process	V(D)J recombination	IBA
GO:0033151	Process	V(D)J recombination	IEA
GO:0033151	Process	V(D)J recombination	ISS
GO:0035091	Function	Phosphatidylinositol binding	IEA
GO:0035091	Function	Phosphatidylinositol binding	ISS
GO:0035265	Process	Organ growth	IEA
GO:0042742	Process	Defense response to bacterium	IEA
GO:0043325	Function	Phosphatidylinositol-3,4-bisphosphate binding	IEA
GO:0043325	Function	Phosphatidylinositol-3,4-bisphosphate binding	ISS
GO:0043565	Function	Sequence-specific DNA binding	IBA
GO:0046622	Process	Positive regulation of organ growth	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0080025	Function	Phosphatidylinositol-3,5-bisphosphate binding	IEA
GO:0080025	Function	Phosphatidylinositol-3,5-bisphosphate binding	ISS
GO:0097519	Component	DNA recombinase complex	IBA
GO:0140002	Function	Histone H3K4me3 reader activity	IEA
GO:0140002	Function	Histone H3K4me3 reader activity	ISS
GO:1904155	Process	DN2 thymocyte differentiation	IEA

Other IDs

• MIM: 179616
• HGNC: 9832
• e!Ensembl: ENSG00000175097

Protein

• UniProt ID: P55895
• Protein name: V(D)J recombination-activating protein 2 (RAG-2)
• Protein function: Core component of the RAG complex, a multiprotein complex that mediates the DNA cleavage phase during V(D)J recombination. V(D)J recombination assembles a diverse repertoire of immunoglobulin and T-cell receptor genes in developing B and T-lymph
• PDB: 8T4R
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF03089	RAG2	51 → 389	Recombination activating protein 2	Family
  PF13341	RAG2_PHD	414 → 491	RAG2 PHD domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Cells of the B- and T-lymphocyte lineages.
• Sequence:

  MSLQMVTVSNNIALIQPGFSLMNFDGQVFFFGQKGWPKRSCPTGVFHLDVKHNHVKLKPT
  IFSKDSCYLPPLRYPATCTFKGSLESEKHQYIIHGGKTPNNEVSDKIYVMSIVCKNNKKV
  TFRCTEKDLVGDVPEARYGHSINVVYSRGKSMGVLFGGRSYMPSTHRTTEKWNSVADCLP
  CVFLVDFEFGCATSYILPELQDGLSFHVSIAKNDTIYILGGHSLANNIRPANLYRIRVDL
  PLGSPAVNCTVLPGGISVSSAILTQTNNDEFVIVGGYQLENQKRMICNIISLEDNKIEIR
  EMETPDWTPDIKHSKIWFGSNMGNGTVFLGIPGDNKQVVSEGFYFYMLKCAEDDTNEEQT
  TFTNSQTSTEDPGDSTPFEDSEEFCFSAEANSFDGDDEFDTYNEDDEEDESETGYWITCC
  PTCDVDINTWVPFYSTELNKPAMIYCSHGDGHWVHAQCMDLAERTLIHLSAGSNKYYCNE
  HVEIARALHTPQRVLPLKKPPMKSLRKKGSGKILTPAKKSFLRRLFD

• Sequence length: 527

Pathways

KEGG:

FoxO signaling pathway
Primary immunodeficiency

Reactome:

MAPK6/MAPK4 signaling

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Atypical severe combined immunodeficiency due to complete RAG1/2 deficiency	Likely pathogenic; Pathogenic	rs1064793251, rs148508754, rs193922573, rs1204766339	RCV000681583 RCV000681571 RCV000681592 RCV000681600
Combined immunodeficiency with skin granulomas	Pathogenic; Likely pathogenic	rs1851074701, rs121917894, rs1406618487, rs2133312873, rs2133311139, rs1470797202, rs2133313100, rs1851074524, rs2133313784, rs1315729938, rs764485070, rs1440633758, rs2133316487, rs2133313716, rs370666759, rs2133314424, rs755941834, rs756676209, rs754975137, rs2133314621, rs2133313582, rs1564997121, rs2133312509, rs1342428152, rs1851081720, rs756192655, rs1224542443, rs786205616, rs2494799758, rs2494801025, rs2494794434, rs2494786655, rs2494791063, rs2494787994, rs2494788127, rs2494799074, rs193922574, rs121917895, rs36001797, rs121918574, rs121918575, rs750849852, rs2494791806, rs2494799242, rs2494795418, rs1174918583, rs1397294905, rs2494788679, rs756694972, rs1336686317, rs2494799990, rs2494789497, rs1434109608, rs746734641, rs762054841, rs2494791448, rs1564995465, rs2494790291, rs2494797251, rs773710101, rs2494788285, rs2494798134, rs2494793071, rs2494792018, rs2494800686, rs2494791825, rs2494794279, rs2494800701, rs1064793250, rs909264507, rs148508754, rs193922572, rs193922573, rs748727021, rs1204766339, rs1564995627, rs765298019, rs1564997563, rs879541124, rs768567592, rs1590713653, rs147155709, rs1335036396, rs1851096223, rs1851098227, rs1434362838, rs1164927451, rs1851062418, rs1851080959	RCV001313623 RCV001331314 RCV001379226 RCV001379080 RCV001381106 RCV001389164 RCV001389866 RCV001389166 RCV001380349 RCV001386499 RCV001869833 RCV001943182 RCV001872560 RCV001998712 RCV001950680 RCV002002843 RCV001949224 RCV001953825 RCV002022809 RCV001999973 RCV002040484 RCV001957944 RCV001950972 RCV002030270 RCV001982896 RCV001963293 RCV002043766 RCV003061066 RCV003058303 RCV001852070 RCV002577362 RCV002847102 RCV002851216 RCV002835369 RCV002894152 RCV002866079 RCV002898572 RCV003013237 RCV003031080 RCV001049147 RCV001851843 RCV001043887 RCV000014019 RCV000014020 RCV003472565 RCV003472566 RCV003472567 RCV003463446 RCV003463447 RCV003463448 RCV003463449 RCV003471783 RCV003463450 RCV003785398 RCV003790464 RCV003786917 RCV003791901 RCV003793654 RCV003801195 RCV003796928 RCV003794767 RCV003809722 RCV003810005 RCV003815428 RCV003815564 RCV003807527 RCV004574683 RCV004574684 RCV004574685 RCV004574686 RCV004574687 RCV004574688 RCV004574689 RCV001865427 RCV002496885 RCV005042098 RCV001389165 RCV005042099 RCV001059752 RCV000547792 RCV000681600 RCV001389163 RCV001042148 RCV000681575 RCV001219165 RCV001220628 RCV000645685 RCV000806149 RCV005225063 RCV001046638 RCV001041863 RCV001063030 RCV003473774 RCV001224669 RCV001205818 RCV001203140
Common variable immunodeficiency	Pathogenic	rs121918575, rs1590715754	RCV001027616 RCV001027617
Histiocytic medullary reticulosis	Pathogenic; Likely pathogenic	rs1851074524, rs1315729938, rs764485070, rs2494794434, rs121917894, rs121917895, rs121917896, rs36001797, rs121917897, rs121918575, rs750849852, rs2494788679, rs756694972, rs909264507, rs148508754, rs193922572, rs193922573, rs193922574, rs748727021, rs1204766339, rs1564995611, rs1564995627, rs1564995662, rs773710101, rs754413772, rs765298019, rs1564997121, rs768567592, rs1590713653, rs147155709, rs1335036396, rs1434362838	RCV002499812 RCV001826170 RCV002503333 RCV005045007 RCV000014011 RCV000014012 RCV000014013 RCV000014014 RCV000014018 RCV005042040 RCV005047611 RCV005047612 RCV005047613 RCV002496885 RCV005042098 RCV000030396 RCV005042099 RCV001831615 RCV001834778 RCV000681600 RCV000681599 RCV000681598 RCV001331311 RCV000681594 RCV000681593 RCV000681587 RCV000681581 RCV000681572 RCV001835894 RCV001104242 RCV005610823 RCV001832439 RCV002491690
Inborn error of immunity	Pathogenic; Likely pathogenic	rs121917894, rs121917895, rs121917896, rs121917897, rs121918574, rs121918575, rs1064793251, rs909264507, rs148508754, rs193922572, rs193922573, rs1204766339, rs1564995611, rs1564995627, rs1564995660, rs1564995662, rs773710101, rs754413772, rs765298019, rs1479328926, rs1564997121, rs1564997563	RCV000681586 RCV000681574 RCV000681589 RCV000681573 RCV000681578 RCV000681597 RCV000681583 RCV000681576 RCV000681571 RCV000681591 RCV000681592 RCV000681600 RCV000681599 RCV000681598 RCV000681596 RCV000681595 RCV000681594 RCV000681593 RCV000681587 RCV000681584 RCV000681581 RCV000681575 RCV000681572
RAG2-related disorder	Pathogenic; Likely pathogenic	rs148508754, rs193922572	RCV004755751 RCV003407371 RCV003420026
Recombinase activating gene 2 deficiency	Pathogenic; Likely pathogenic	rs1851074524, rs1440633758, rs754975137, rs2494801025, rs121917894, rs121917895, rs121917896, rs36001797, rs121917897, rs121918574, rs121918575, rs1064793251, rs909264507, rs148508754, rs193922572, rs193922573, rs193922574, rs1204766339, rs1564995611, rs1564995627, rs1564995660, rs1564995662, rs773710101, rs754413772, rs765298019, rs1479328926, rs1564997121, rs1564997563, rs879541124, rs1590713653, rs1164927451	RCV003399209 RCV003401875 RCV005635371 RCV003991484 RCV000681586 RCV000681574 RCV000681589 RCV003398500 RCV000681573 RCV000681578 RCV000681597 RCV000681583 RCV000681576 RCV000681571 RCV000681591 RCV000681592 RCV003325303 RCV000681600 RCV000681599 RCV000681598 RCV000681596 RCV003991476 RCV000681594 RCV000681593 RCV000681587 RCV000681584 RCV000681581 RCV000681575 RCV000681572 RCV003403398 RCV003492174 RCV005633963
Severe combined immunodeficiency disease	Likely pathogenic; Pathogenic	rs764485070, rs1224542443, rs121917896, rs121918575, rs1064793250, rs909264507, rs148508754, rs193922574, rs1590713653, rs1335036396	RCV005432805 RCV006262341 RCV005237374 RCV001731284 RCV005431692 RCV003226307 RCV000030395 RCV001731320 RCV005056255 RCV005902013 RCV005912480
Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-positive	Pathogenic; Likely pathogenic	rs1851074701, rs121917894, rs1406618487, rs2133312873, rs2133311139, rs1470797202, rs2133313100, rs1851074524, rs2133313784, rs1315729938, rs2133315462, rs764485070, rs1440633758, rs2133316487, rs2133313716, rs370666759, rs2133314424, rs755941834, rs756676209, rs754975137, rs2133314621, rs2133313582, rs1564997121, rs2133312509, rs1342428152, rs1851081720, rs756192655, rs1224542443, rs786205616, rs2494799758, rs2494801025, rs2494794434, rs2494786655, rs2494791063, rs2494787994, rs2494788127, rs2494799074, rs193922574, rs121917895, rs36001797, rs121917897, rs121918575, rs750849852, rs2494791806, rs2494795418, rs2494788679, rs756694972, rs2494799990, rs2494789497, rs1434109608, rs746734641, rs762054841, rs2494791448, rs1564995465, rs2494790291, rs2494797251, rs773710101, rs2494788285, rs2494798134, rs1064793250, rs909264507, rs148508754, rs193922572, rs193922573, rs748727021, rs1204766339, rs1564995627, rs1564995660, rs765298019, rs879541124, rs768567592, rs1590713653, rs147155709, rs1335036396, rs1851096223, rs1851098227, rs1434362838, rs1164927451, rs1851062418, rs1851080959	RCV001313623 RCV003227962 RCV001379226 RCV001379080 RCV001381106 RCV001389164 RCV001389866 RCV001389166 RCV001380349 RCV001386499 RCV001580771 RCV001824243 RCV001943182 RCV001872560 RCV001998712 RCV001950680 RCV002002843 RCV001949224 RCV001953825 RCV002022809 RCV001999973 RCV002040484 RCV001957944 RCV001950972 RCV002030270 RCV001982896 RCV001963293 RCV002043766 RCV003061066 RCV003058303 RCV001852070 RCV002577362 RCV002847102 RCV002851216 RCV002835369 RCV002894152 RCV002866079 RCV002898572 RCV003013237 RCV003031080 RCV000681586 RCV000681574 RCV001043887 RCV000681573 RCV000821298 RCV005047611 RCV003779085 RCV003779086 RCV005047612 RCV005047613 RCV003785398 RCV003790464 RCV003786917 RCV003791901 RCV003793654 RCV003801195 RCV003796928 RCV003794767 RCV003809722 RCV003810005 RCV003815428 RCV003815564 RCV003807527 RCV001865427 RCV000681576 RCV005042098 RCV001389165 RCV005042099 RCV001059752 RCV000547792 RCV001378887 RCV001389163 RCV002283492 RCV000681587 RCV000681572 RCV001220628 RCV000645685 RCV000806149 RCV005225063 RCV001046638 RCV001041863 RCV001063030 RCV001220928 RCV001224669 RCV001205818 RCV001203140
Severe combined immunodeficiency, B cell-negative	Pathogenic; Likely pathogenic	rs121917894, rs2133313409, rs121917897, rs1564995662	RCV000014010 RCV000014015 RCV000014017 RCV004527390

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Immunodeficiency 104	Conflicting classifications of pathogenicity	rs762407838	RCV001815003

Associations from Text Mining
Disease Name	Relationship Type	References
Arthritis Rheumatoid	Associate	19404965
Arthrogryposis	Associate	20128425
Autoimmune Diseases	Associate	24290284, 26186701, 30307608, 31388879, 34664192
Common Variable Immunodeficiency	Associate	26186701
Congenital Hereditary and Neonatal Diseases and Abnormalities	Associate	30307608
Death	Associate	20128425
Drug Resistant Epilepsy	Associate	34664192
Eosinophilia	Associate	31885011, 9630231
Epstein Barr Virus Infections	Associate	26186701
Exanthema	Associate	31885011
Granuloma	Associate	18463379, 31885011
Granulomatous Disease Chronic	Associate	33954879
Hepatitis B	Associate	11313270, 20128425
Immune System Diseases	Associate	31388879
Immunologic Deficiency Syndromes	Associate	10891502, 18463379, 26186701, 30307608, 31388879, 9630231
Immunologic Deficiency Syndromes	Inhibit	34664192
Infections	Associate	34664192
Inflammation	Associate	34664192
Leukemia	Associate	34982829
Leukemia Lymphocytic Chronic B Cell	Stimulate	27198500
Lupus Erythematosus Systemic	Associate	12115231, 17608810
Lymphoma B Cell	Associate	7494341
Lymphopenia	Associate	26186701
Mycobacterium Infections Nontuberculous	Associate	33954879
Neointima	Associate	24290284
Neoplasms	Associate	17511028, 21655267, 24853685
Otitis Media	Associate	26186701
Pemphigus	Associate	32926429
Pneumonia	Associate	26186701
Primary Immunodeficiency Diseases	Associate	10891502, 24290284, 34622798, 34786962
Recombinant chromosome 8 syndrome	Associate	29772310, 37891182
Severe Combined Immunodeficiency	Associate	10606976, 10777560, 11313270, 11359901, 11520796, 16276422, 19912631, 20128425, 22295088, 24290284, 26186701, 28266921, 29051008, 29772310, 30307608, 31885011, 32265901, 32691468, 32754152, 33954879, 35303369, 36279417, 36786340, 9630231
Sezary Syndrome	Associate	27039262
Sinusitis	Associate	26186701
Spastic Paraplegia Hereditary	Associate	10891502
Tertiary Lymphoid Structures	Associate	11160277
Tetra amelia with ectodermal dysplasia and lacrimal duct abnormalities	Associate	34982829
Thyroid Cancer Papillary	Associate	21909078
Vasculitis Leukocytoclastic Cutaneous	Associate	26186701
Waldenstrom Macroglobulinemia	Associate	27301862
X Linked Combined Immunodeficiency Diseases	Associate	16276422, 21625022, 22424479, 26186701, 29051008, 31885011, 32691468, 36279417